Mercurial > repos > bgruening > deeptools_plot_pca
comparison plotPCA.xml @ 21:93ce2662f917 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
author | bgruening |
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date | Wed, 22 Aug 2018 17:00:56 -0400 |
parents | d9376d223fad |
children | c899e0ccff8c |
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20:aca788d8e71d | 21:93ce2662f917 |
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1 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0"> | 1 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0" profile="18.01"> |
2 <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description> | 2 <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description> |
3 <macros> | 3 <macros> |
4 <token name="@BINARY@">plotPCA</token> | 4 <token name="@BINARY@">plotPCA</token> |
5 <import>deepTools_macros.xml</import> | 5 <import>deepTools_macros.xml</import> |
6 </macros> | 6 </macros> |
20 $advancedOpt.transpose | 20 $advancedOpt.transpose |
21 $advancedOpt.rowCenter | 21 $advancedOpt.rowCenter |
22 #if $advancedOpt.colors: | 22 #if $advancedOpt.colors: |
23 --colors $advancedOpt.colors | 23 --colors $advancedOpt.colors |
24 #end if | 24 #end if |
25 #if $advancedOpt.markers: | |
26 --markers $advancedOpt.markers | |
27 #end if | |
25 #end if | 28 #end if |
26 #if $outFileNameData | 29 #if $outFileNameData |
27 --outFileNameData '$output_outFileNameData' | 30 --outFileNameData '$output_outFileNameData' |
28 #end if | 31 #end if |
29 ]]> | 32 ]]> |
38 <option value="no" selected="true">no</option> | 41 <option value="no" selected="true">no</option> |
39 <option value="yes">yes</option> | 42 <option value="yes">yes</option> |
40 </param> | 43 </param> |
41 <when value="no" /> | 44 <when value="no" /> |
42 <when value="yes"> | 45 <when value="yes"> |
43 <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" /> | 46 <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" /> |
44 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text" | 47 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text" |
45 help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." /> | 48 help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." /> |
46 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer" | 49 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer" |
47 help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." /> | 50 help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." /> |
48 <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." /> | 51 <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." /> |
49 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" /> | 52 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" /> |
50 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" /> | 53 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" /> |
51 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True" | 54 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True" |
52 help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." /> | 55 help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." /> |
56 <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True" | |
57 help="A list of markers for the symbols. (e.g., '<','>','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." /> | |
53 </when> | 58 </when> |
54 </conditional> | 59 </conditional> |
55 </inputs> | 60 </inputs> |
56 <outputs> | 61 <outputs> |
57 <expand macro="output_image_file_format_not_nested" /> | 62 <expand macro="output_image_file_format_not_nested" /> |